2BHI | pdb_00002bhi

Crystal structure of Taiwan cobra cardiotoxin A3 complexed with sulfogalactoceramide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H0J	PDB ENTRY 1H0J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		1.8 M SODIUM MALONATE, 7.5% (V/V) TERT-BUTANOL, 7.5% (V/V) PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), 0.08% (W/V) C10E6, 50 MM IMIDAZOLE, AND 50 MM TRIS-HCL, PH 7.0.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.327	α = 90
b = 63.327	β = 90
c = 120.879	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD	MIRRORS	2004-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL17B2		NSRRC	BL17B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	26.5	99.8	0.05	34.6	6.1		6821		2	25.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.4	100		0.34	5.1	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1H0J	2.31	26.47	2	6126	501	90	0.219	0.219	0.22	0.222	0.23	RANDOM	40.4

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.31	3.08		2.31		-4.63

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.6
c_improper_angle_d	3.44
c_scangle_it	2.27
c_mcangle_it	1.94
c_angle_deg	1.7
c_scbond_it	1.59
c_mcbond_it	1.22
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	930
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	246

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing